3v Running Log for JobId '2019.jan08.bab'

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  • host ip address=14.139.155.243 (Wed Jan 9 02:14:55 2019)
  • converting pdb into xyzr (Wed Jan 9 02:14:55 2019)
  • completed conversion of PDB file: 2019.jan08.bab.pdb (size: 441k) (Wed Jan 9 02:15:05 2019)
  • converted 14112 atoms of 14112 atoms (Wed Jan 9 02:15:05 2019)
  • found 14112 atoms in pdb (Wed Jan 9 02:15:05 2019)
  • running 3v volume program (Wed Jan 9 02:15:05 2019)
  • smoothing out volume (Wed Jan 9 02:15:05 2019)
  • imaging volume (download mrc) with UCSF Chimera (Wed Jan 9 02:15:06 2019)
  • UCSF Chimera created Jmol compatible file (Wed Jan 9 02:15:17 2019)
  • compressing 2019.jan08.bab.obj (Wed Jan 9 02:15:17 2019)
  • UCSF Chimera completed in 11.93 sec (Wed Jan 9 02:15:17 2019)
  • analyzing volume (Wed Jan 9 02:15:17 2019)
  • normal CoM (13.8, -2.0, -12.9) Å (Wed Jan 9 02:15:24 2019)
  • reduced center failed (Wed Jan 9 02:15:25 2019)
  • volume analysis completed in 7.74 sec (Wed Jan 9 02:15:25 2019)
  • compressing 2019.jan08.bab.mrc (Wed Jan 9 02:15:25 2019)
  • FINISHED (Wed Jan 9 02:15:25 2019)

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Log file display

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Terminal display
		
/srv/output/2019/jan08/bab 
Message: completed conversion of PDB file: 2019.jan08.bab.pdb (size: 441k) 
Message: converted 14112 atoms of 14112 atoms 
Message: found 14112 atoms in pdb 
Message: running 3v volume program 
wrote to mrc file: /var/www/html/3vee/output/2019/jan08/bab/2019.jan08.bab.mrc 
Message: smoothing out volume 
Message: imaging volume UCSF Chimera 
/var/www/html/py/appionlib/apChimSnapshot.py 
Message: UCSF Chimera created Jmol compatible file 
Message: compressing 2019.jan08.bab.obj 
Message: UCSF Chimera completed in 11.93 sec 
OBJFILE /var/www/html/3vee/output/2019/jan08/bab/2019.jan08.bab.obj.gz 
Message: analyzing volume 
Message: normal CoM (13.8, -2.0, -12.9) Å 
Message: reduced center failed 
Message: volume analysis completed in 7.74 sec 
Message: compressing 2019.jan08.bab.mrc 
Message: FINISHED 
		


Citation:
'3V: cavity, channel and cleft volume calculator and extractor' (free text)
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562
by Neil R. Voss and Mark Gerstein
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If you find this useful or want more functionality please contact Neil <vossman77 [at] gmail [dot] com>
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